Align D-xylose reductase (EC 1.1.1.307) (characterized)
to candidate H281DRAFT_01572 H281DRAFT_01572 Predicted oxidoreductase
Query= BRENDA::F2YCN5 (340 letters) >FitnessBrowser__Burk376:H281DRAFT_01572 Length = 339 Score = 139 bits (351), Expect = 8e-38 Identities = 95/319 (29%), Positives = 162/319 (50%), Gaps = 22/319 (6%) Query: 24 TRVALG--TWAIGGWMWG---GTDDDASIKTIHRAIDLGINIIDTAPAYGRGHAEEVVGK 78 +R++LG T+ G +WG G + D + + + A++ G+N+IDTA AY +G +EEVVG Sbjct: 14 SRLSLGAMTFGAGSGIWGSIAGLNSDQAARLVAMAVERGVNLIDTADAYSQGRSEEVVGH 73 Query: 79 AIKG---QRDNLIIATKVGLDWTLTPDQSMRRNSSASRIKKEIEDSLRRLGTDYIDLYQV 135 +K D +++ATKV L T S I + +E SL+RLG D+IDL+Q+ Sbjct: 74 VLKALGLDEDRMLVATKVRLR---TGTGQNEVGLGRSHIMRSVETSLKRLGRDHIDLFQL 130 Query: 136 HWPDPLVPIEETATILEALRKEGKIRSIGVSNYSVQQMDEF------KKYAELAVSQSPY 189 H D LVP++ET +L+ L +GK+R IGV N+S ++ A + +Q Y Sbjct: 131 HDRDALVPLDETLRVLDDLVTQGKVRHIGVCNFSAGDLERAVGITSRTDRAHVVSNQVHY 190 Query: 190 NLFEREIDKDILPYAKKNDLVVLGYGALCRGLLSGRMTADRAFTGDDLRKTDPKFQKPRF 249 +L R+I+ +I+P A N + + + L G LSG+ + + G + P R Sbjct: 191 SLTSRDIEHEIMPVAATNRIGLFVWSPLAGGYLSGKYSQNGGAAGRRAKLDFPPVDTVRA 250 Query: 250 EHYLAAVEELKKLAKEHYNKSVLALAIRWML-EQGPTLALWGACKPEQIDGIDEVFGWQI 308 E LA + E+ + + +++ W+L + T + GA EQ+ + + Sbjct: 251 EPILAVLREVAR----ELAATPAQVSLGWLLAREQITSVIVGARTCEQLAANLDAQNLAL 306 Query: 309 SDEDLKQIDAILAKNIPNP 327 + E ++D + ++P P Sbjct: 307 TSEQCARLDKVSEPSVPFP 325 Lambda K H 0.317 0.136 0.407 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 278 Number of extensions: 14 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 340 Length of database: 339 Length adjustment: 28 Effective length of query: 312 Effective length of database: 311 Effective search space: 97032 Effective search space used: 97032 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory